Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:31:07 GMT 2023 |
| BAM file: | SRX7354245.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | yes |
| Protocol: | strand-specific-reverse |
| Sorting performed: | yes |
Summary
Reads alignment
| Number of mapped reads (left/right): | 41,221,056 / 41,195,930 |
| Number of aligned pairs (without duplicates): | 41,192,887 |
| Total number of alignments: | 88,541,497 |
| Number of secondary alignments: | 6,124,511 |
| Number of non-unique alignments: | 9,880,692 |
| Aligned to genes: | 69,580,110 |
| Ambiguous alignments: | 224,208 |
| No feature assigned: | 8,230,866 |
| Missing chromosome in annotation: | 625,621 |
| Not aligned: | 2,354,474 |
Reads genomic origin
| Exonic: | 69,580,110 / 89.42% |
| Intronic: | 5,015,738 / 6.45% |
| Intergenic: | 3,215,128 / 4.13% |
| Intronic/intergenic overlapping exon: | 2,511,066 / 3.23% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.81 |
Junction analysis
| Reads at junctions: | 20,845,453 |
| ACCT | 5.34% |
| AGGT | 4.7% |
| ATCT | 3.71% |
| AGGA | 3.52% |
| TCCT | 3.41% |
| GCCT | 3.25% |
| AGCT | 2.8% |
| CCCT | 2.65% |
| AGGC | 2.36% |
| TTCT | 2.27% |
| AGAT | 2.2% |
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